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Update ONT_pilot_w_GDB_samples authored by Susheel Busi's avatar Susheel Busi
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ONT_pilot_w_GDB_samples.md
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...@@ -1051,8 +1051,8 @@ make test && make install ...@@ -1051,8 +1051,8 @@ make test && make install
##### PLASMIDS ##### ##### PLASMIDS #####
- LDN is running PathoFact on the ONT samples, so obtained the plasmid data through the ```MGE/plasmid/$i_plasmids_selected.tsv``` file generated in PathoFact - LDN is running PathoFact on the ONT samples, so obtained the plasmid data through the ```MGE/plasmid/$i_plasmids_selected.tsv``` file generated in PathoFact
- checking the number of plasmids in the assemblies
``` ```
# checking the number of plasmids in the assemblies
# grep -hnr "plasmid" $i_plasflow_prediction_final.tsv > $i_plasmids_selected.tsv # grep -hnr "plasmid" $i_plasflow_prediction_final.tsv > $i_plasmids_selected.tsv
for file in /scratch/users/ldenies/ONT/PathoFact/PathoFact_results/MGE/plasmid/*final.tsv for file in /scratch/users/ldenies/ONT/PathoFact/PathoFact_results/MGE/plasmid/*final.tsv
......